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Crystal structure of creatinine amidohydrolase (creatininase)

Analyse Crystal structure of creatinine amidohydrolase (creatininase) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Q3K
Type: protein
Length: 1,554 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Creatininase
EC: 3.5.2.10
UniProt: P83772
Ligands: ZN
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Creatininase (EC 3.5.2.10)	protein	259	47% helix, 12% strand	P83772

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1074	0.82	0.83	87	empty
2	983	0.78	0.80	68	empty
3	1014	0.78	0.80	63	empty
4	978	0.78	0.80	62	empty
5	58	0.74	0.99	14	GOL

Interfaces

12 interfaces between chains.

A–B · 1984 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 1980 Å² buried · 45 hydrogen bonds · protein-protein
C–D · 1978 Å² buried · 42 hydrogen bonds · protein-protein
D–E · 1527 Å² buried · 34 hydrogen bonds · protein-protein
A–F · 1511 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

1Q3K · Crystal structure of creatinine amidohydrolase (creatininase) · the same entry in another collection · chain F against F, TM-score 1.00
P83772 · AlphaFold monomer V2.0 prediction for creatinine amidohydrolase (P83772) · a predicted model of the same protein · chain F against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P83772
Elsewhere: RCSB PDB 1Q3K · PDBe 1Q3K · UniProt P83772

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